{"id":"NHA000078","research":"hum0014","url":"https://humandbs.dbcls.jp/dataset/NHA000078","datePublished":"2019-01-25","dateModified":"2019-01-25","values":[{"key":"access-criteria","label":{"ja":"アクセス制限","en":"Access criteria"},"type":"vocabulary","terms":[{"code":"unrestricted-access","label":{"ja":"非制限公開","en":"Unrestricted-access"}}]},{"key":"type-of-data","label":{"ja":"データの種類","en":"Type of data"},"type":"text","text":{"ja":"2型糖尿病36,614症例および\n対照者155,150名のGWASメタ解析","en":"meta analysis of 4 GWASs for T2DM"}}],"experiments":[{"label":"Genotyping by array","values":[{"key":"materials-and-participants","label":{"ja":"材料と対象者","en":"Materials and participants"},"type":"text","text":{"ja":"[GWAS-1]\n2型糖尿病（ICD-10：E11）：9,804症例、対照者：6,728名\n[GWAS-2]\n2型糖尿病（ICD-10：E11）：5,639症例、対照者：19,407名\n[GWAS-3]\n2型糖尿病（ICD-10：E11）：18,688症例、対照者：121,950名\n[GWAS-4]\n2型糖尿病（ICD-10：E11）：2,483症例、対照者：7,065名","en":"[GWAS-1]\n- 9,804 T2DM patients (ICD-10: E11)\n- 6,728 controls\n[GWAS-2]\n- 5,639 T2DM patients (ICD-10: E11)\n- 19,407 controls\n[GWAS-3]\n- 18,688 T2DM patients (ICD-10: E11)\n- 121,950 controls\n[GWAS-4]\n- 2,483 T2DM patients (ICD-10: E11)\n- 7,065 controls"}},{"key":"disease","label":{"ja":"疾患","en":"Disease"},"type":"disease","diseases":[{"terms":[{"code":"E11","label":{"ja":"２型＜インスリン非依存性＞糖尿病＜NIDDM＞","en":"Type 2 diabetes mellitus"}}],"name":{"ja":"2型糖尿病","en":"T2DM patients"}}]},{"key":"health-status","label":{"ja":"健康状態","en":"Health status"},"type":"vocabulary","terms":[{"code":"mixed","label":{"ja":"混在","en":"Mixed"}}]},{"key":"subject-count","label":{"ja":"対象者数","en":"Subject count"},"type":"number","numbers":[{"value":191764,"unit":null,"high":null}]},{"key":"subject-count-type","label":{"ja":"対象者数の数え方","en":"Counted as"},"type":"vocabulary","terms":[{"code":"individual","label":{"ja":"人数","en":"Individual"}}]},{"key":"sample-description","label":{"ja":"試料説明","en":"Sample description"},"type":"text","text":{"ja":"末梢血から抽出したgDNA","en":"gDNA extracted from peripheral blood cells"}},{"key":"tissue","label":{"ja":"組織","en":"Tissue"},"type":"vocabulary","terms":[{"code":"peripheral-blood","label":{"ja":"末梢血","en":"Peripheral blood"}}]},{"key":"is-tumor","label":{"ja":"腫瘍 / 非腫瘍","en":"Tumor / normal"},"type":"vocabulary","terms":[{"code":"normal","label":{"ja":"非腫瘍","en":"Normal"}}]},{"key":"sample-provider","label":{"ja":"試料の入手元","en":"Sample provider"},"type":"text","text":{"ja":null,"en":null}},{"key":"experimental-method","label":{"ja":"実験方法","en":"Experimental method"},"type":"vocabulary","terms":[{"code":"genotyping-by-array","label":{"en":"Genotyping by array"}}]},{"key":"targets","label":{"ja":"測定対象","en":"Target"},"type":"text","text":{"ja":null,"en":null}},{"key":"reagents","label":{"ja":"試薬キット","en":"Reagent kit"},"type":"vocabulary","terms":[{"code":"humanomniexpress-beadchip-kit","label":{"en":"HumanOmniExpress BeadChip Kit"}},{"code":"humanexome-beadchip-kit","label":{"en":"HumanExome BeadChip Kit"}},{"code":"humanomniexpressexome-beadchip-kit","label":{"en":"HumanOmniExpressExome BeadChip Kit"}},{"code":"human610-quad-beadchip-kit","label":{"en":"Human610-Quad BeadChip Kit"}}]},{"key":"platform","label":{"ja":"プラットフォーム","en":"Platform"},"type":"vocabulary","terms":[{"code":"illumina-humanomniexpress","label":{"en":"Illumina HumanOmniExpress"}},{"code":"illumina-humanexome","label":{"en":"Illumina HumanExome"}},{"code":"illumina-humanomniexpressexome","label":{"en":"Illumina HumanOmniExpressExome"}},{"code":"illumina-human610-quad","label":{"en":"Illumina Human610-Quad"}}]},{"key":"reference-sequence","label":{"ja":"参照ゲノム","en":"Reference genome"},"type":"vocabulary","terms":[{"code":"grch37","label":{"en":"GRCh37"}}]},{"key":"filtering","label":{"ja":"QC・フィルタリング","en":"QC and filtering"},"type":"text","text":{"ja":"GenotypingのQC：\nGWAS1, GWAS3, GWAS4除外基準\n(i) hetero count < 5\n(ii) 各chipでHWE P < 1.0 × 10^-6\n(iii) in-house WGSデータとのジェノタイプ一致率 < 0.99\n(iv) SNV call rate < 0.99\n\nGWAS2除外基準\n(i) SNV call rate < 0.99\n(ii) MAF < 0.01\n(iii) differential missingness P < 1.0 × 10^-6\n(iv) HWE P < 1.0 × 10^-6\n\nImputationのQC：\nリファレンスパネルで HWE P < 1 × 10^-6 もしくは MAF < 0.01を除外\n3つ以上のGWASでImputation quality (Rsq) < 0.3となったものを除外","en":"Genotyping QC:\nexclusion criteria of GWAS1, GWAS3, GWAS4\n(i) hetero count < 5\n(ii) HWE P < 1.0 × 10^-6 on each chip\n(iii) genotype concordance rate < 0.99 with in-house WGS data\n(iv) SNV call rate < 0.99\n\nexclusion criteria of GWAS2\n(i) SNV call rate < 0.99\n(ii) MAF < 0.01\n(iii) differential missingness P < 1.0 × 10^-6\n(iv) HWE P < 1.0 × 10^-6\n\nImputation QC:\nHWE P < 1 × 10^-6 or MAF < 0.01 in the reference panel\nImputation quality (Rsq) < 0.3 in more than two GWAS"}},{"key":"imputation","label":{"ja":"インピュテーション","en":"Imputation"},"type":"text","text":{"ja":"minimac [imputation(1000 genomes Phase 3)]","en":"minimac [imputation(1000 genomes Phase 3)]"}},{"key":"analysis-methods","label":{"ja":"解析方法","en":"Analysis method"},"type":"text","text":{"ja":"GenCall software（GenomeStudio）","en":"GenCall software (GenomeStudio)"}},{"key":"variant-number","label":{"ja":"バリアント数","en":"Variant count"},"type":"number","numbers":[{"value":12557761,"unit":null,"high":null,"suffix":{"ja":" SNPs","en":" SNPs"}}]},{"key":"processed-data-type","label":{"ja":"加工データの種類","en":"Processed data type"},"type":"vocabulary","terms":[{"code":"gwas-summary-statistics","label":{"ja":"GWAS 要約統計量","en":"GWAS summary statistics"}}]},{"key":"has-phenotype-data","label":{"ja":"表現型データの有無","en":"Phenotype data"},"type":"vocabulary","terms":[{"code":"included","label":{"ja":"あり","en":"Included"}}]},{"key":"policies","label":{"ja":"利用ポリシー","en":"Data use policy"},"type":"vocabulary","terms":[{"code":"nbdc-data-sharing-policy-jgap000001","label":{"ja":"NBDC データ共有ポリシー (JGAP000001)","en":"NBDC data sharing policy (JGAP000001)"}}]}]}],"fileFormats":[{"code":"xlsx","label":{"en":"XLSX"}},{"code":"zip","label":{"en":"ZIP"}}]}